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Genomic analysis uncovers functional variation in the c-terminus of anthocyanin-activating MYB transcription factors

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Horticulture Research 2021年第1期8卷 885-898页

作者： Jessica A.Rodrigues Richard V.Espley andrew c.allan The New Zealand Institute for Plant and Food Research Limited 120 Mount Albert RoadSandringhamAuckland 1025New Zealand School of Biological Sciences University of Auckland3A Symonds StAuckland 1010New Zealand

MYB transcription factors regulate diverse aspects of plant development and secondary metabolism,often by partnering in transcriptional regulatory ***,we harness genomic resources to identify novel MYBs,thereby producing an updated eudicot MYB phylogeny with revised relationships among subgroups as well as new information on sequence variation in the disordered c-terminus of anthocyanin-activating ***®and hidden Markov model scans of gene annotations identified a total of 714 MYB transcription factors across the genomes of four crops that span the eudicots:apple,grape,kiwifruit and *** model-based phylogenetic inference identified novel members of previously defined subgroups,and the function of specific anthocyanin-activating subgroup 6 members was assayed transiently in tobacco *** conservation within subgroup 6 highlighted one previously described and two novel short linear motifs in the disordered c-terminal *** novel motifs have a mix of hydrophobic and acidic residues and are predicted to be relatively ordered compared with flanking protein *** of motifs with the Eukaryotic Linear Motif database suggests roles in protein–protein *** of motifs and their flanking regions from strong anthocyanin activators into weak activators,and vice versa,affected *** conclude that,although the MYB c-terminal sequence diverges greatly even within MYB clades,variation within the c-terminus at and near relatively ordered regions offers opportunities for exploring MYB function and developing superior alleles for plant breeding.

关键词： phylogeny metabolism thereby

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Strategies for fast breeding and improvement of Actinidia species

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Horticulture Research 2023年第3期10卷 266-270页

作者： Dinum Herath Tianchi Wang charlotte Voogd Yongyan Peng Mikaela Douglas Joanna Putterill Erika Varkonyi-Gasic andrew c.allan The New Zealand Institute for Plant and Food Research Limited(Plant&Food Research)Mt Albert Private Bag 92169Auckland Mail CentreAuckland 1142New Zealand School of Biological Sciences University of AucklandPrivate Bag 92019AucklandNew Zealand

Perspective Ensuring food security for a rapidly growing world population will need new *** include speed breeding and new breeding technologies,which have been established for major staple *** of woody perennial fruit tree species has progressed at a much slower pace and has met many *** fruit production will face major challenges with climate change,such as the loss of winter chilling needed for f lowering,a potential decrease in pollinator availability,and increasing pest and disease *** chinensis(kiwifruit)is an important fresh fruit crop,with varieties only several generations removed from the wild accessions and carrying only a fraction of the available genetic diversity[1,2].Improvement of traits such as fruit quality and storage,and resistance to emergent diseases underpin the breeding efforts,which are hampered by a long generation time,large plant size,dependence on chilling for budbreak and f lowering,dioecy and different ploidy *** addition to kiwifruit,the genus Actinidia consists of more than 50 species with edible fruit,all showing tremendous potential as future fruit crops[3].Their fast domestication and improvement will enable production of high-quality healthy fruit,contributing to food security in the changing climate conditions.

关键词： breeding crops removed

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Differential regulation of the anthocyanin profile in purple kiwifruit(Actinidia species)

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Horticulture Research 2019年第1期6卷 1746-1761页

作者： Yongyan Peng Kui Lin-Wang Janine M.cooney Tianchi Wang Richard V.Espley andrew c.allan School of Biological Sciences University of AucklandAucklandNew Zealand The New Zealand Institute for Plant and Food Research Limited Mt AlbertAucklandNew Zealand The New Zealand Institute for Plant and Food Research Limited East Street3214 HamiltonNew Zealand

Anthocyanins are a group of secondary metabolites that colour fruit and flowers orange,red,purple or blue depending on a number of factors,such as the basic structure,co-pigmentation,metal ion complexation and vacuolar *** biosynthesis of anthocyanin is regulated at the transcriptional level by a group of transcription factors,the MYB–bHLH–WD40(MBW)*** this study,the purple colouration in several kiwifruit(Actinidia)species was identified and characterised as red cyanidin-based and blue delphinidin-based *** differential pigmentation in the skin and flesh can be attributed to the differential ratio of cyanidin and delphinidin derivatives accumulated in the total anthocyanin *** expression of anthocyanin biosynthetic genes chalcone synthase(cHS),flavonoid 3-O-glucosyltransferase(F3GT),flavonoid 3′-hydroxylase(F3′H)and flavonoid 3′5′-hydroxylase(F3′5′H)is crucial for anthocyanin ***,the balance of expression of the F3′H and F3′5′H genes appears responsible for the ratio of cyanidin and delphinidin derivatives,while a lack of cHS,F3GT and MYB110 expression is responsible for a lack of total *** transcriptional regulation of the F3′H and F3′5′H promoters by the R2R3 MYB transcription factor MYB110 is markedly different in tobacco transient *** kiwifruit MYB10 or MYB110 are over-expressed in Actinidia chinensis both cyanidin-based and delphinidin-based anthocyanins are elevated,but F3′H and F3′5′H genes are not strongly correlated with MYB *** results suggest that the core kiwifruit anthocyanin pathway genes are dependent on characterised MYB transcription factors,while other regulatory proteins are more directly responsible for the expression of the F3′H and F3′5′H genes.

关键词： Actinidia orange flowers

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The involvement of PybZIPa in light-induced anthocyanin accumulation via the activation of PyUFGT through binding to tandem G-boxes in its promoter

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Horticulture Research 2019年第1期6卷 82-94页

作者： Hainan Liu Jun Su Yangfan Zhu Gaifang Yao andrew c.allan charles Ampomah-Dwamena Qun Shu Kui Lin-Wang Shaoling Zhang Jun Wu centre of Pear Engineering Technology Research State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural University210095 NanjingChina Institute of Horticulture Yunnan Academy of Agricultural Sciences650205 KunmingChina The New Zealand Institute for Plant&Food Research Limited AucklandNew Zealand School of Biological Sciences University of AucklandAucklandNew Zealand

To gain insight into how anthocyanin biosynthesis is controlled by light in fruit,transcriptome and metabolome analyses were performed in the chinese sand pear cultivar“Mantianhong”(Pyrus pyrifolia)after bagging and bag *** investigated transcriptional and metabolic changes and gene-metabolite correlation *** tests of anthocyanin content and transcriptional changes revealed that 1,530 transcripts were strongly correlated with 15 anthocyanin derivatives(R2>0.9,P-valuecripts categorized as being associated with flavonoid metabolism,transcriptional regulation,and light *** connection network revealed a new photosensitive transcription factor,PybZIPa,that might play an important role during light-induced anthocyanin *** overexpression of PybZIPa promoted anthocyanin accumulation in pear and strawberry fruit as well as tobacco *** luciferase and Y1H assays further verified that PybZIPa directly activated the expression of PyUFGT by binding to tandem G-box motifs in the promoter,which was key to differential anthocyanin accumulation in debagged pear skin,and the number of G-box motifs affected the transcriptional activation of PyUFGT by *** results indicate that the light-induced anthocyanin biosynthesis regulatory mechanism in pear differs from that described in previous reports suggesting that a bZIP family member co-regulates anthocyanin biosynthesis with other transcription factors in apple and *** was found that,in response to light,PybZIPa promoted anthocyanin biosynthesis by regulating important transcription factors(PyMYB114,PyMYB10,and PyBBX22)as well as structural genes(PyUFGT)via binding to G-boxes within *** activation was amplified by the self-binding of PybZIPa to activate its own ***,we demonstrate the utility of a multiomics integrative approach for discovering new functional genes and pathways underlying light-induced anthocyanin

关键词： cultivar activation metabolism

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DNA methylation controlling abscisic acid catabolism responds to light to mediate strawberry fruit ripening

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Journal of Integrative Plant Biology 2024年第8期66卷 1718-1734页

作者： Yunfan Sun Xiaofang Yang Rongrong Wu Shouzheng Lv Yunduan Li Haoran Jia Yuying Yang Baijun Li Wenbo chen andrew c.allan Guihua Jiang Yan-Na Shi Kunsong chen college of Agriculture&Biotechnology Zhejiang UniversityZijingang CampusHangzhou 310058China Institute of Horticulture Zhejiang Academy of Agricultural SciencesHangzhouZhejiang 310021China Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Zhejiang UniversityZijingang CampusHangzhou 310058China The State Agriculture Ministry Laboratory of Horticultural Plant Growth Development and Quality ImprovementZhejiang UniversityZijingang CampusHangzhou 310058China New Zealand Institute for Plant&Food Research Limited Private Bag 92169AucklandNew Zealand School of Biological Sciences University of AucklandPrivate Bag 92019AucklandNew Zealand

Phytohormones,epigenetic regulation and environmental factors regulate fruit ripening but their interplay during strawberry fruit ripening remains to be *** this study,bagged strawberry fruit exhibited delayed ripening compared with fruit grown in normal light,correlating with reduced abscisic acid(ABA) *** of the key ABA catabolism gene,ABA 8′-hydroxylase FacYP707A4,was induced in bagged *** light exclusion whole genome DNA methylation levels were up-regulated,corresponding to a delayed ripening process,while DNA methylation levels in the promoter of FacYP707A4 were suppressed,correlating with increases in transcript and decreased ABA *** indicated FacRY1,a blue light receptor repressed in bagged fruit and FaAGO4,a key protein involved in RNA-directed DNA methylation,could bind to the promoter of *** interaction between FacRY1 and FaAGO4,and an increased enrichment of FaAGO4 directed to the FacYP707A4 promoter in fruit grown under light suggests FacRY1 may influence FaAGO4 to modulate the DNA methylation status of the FacYP707A4 ***,transient overexpression of FacRY1,or an increase in FacRY1 transcription by blue light treatment,increases the methylation level of the FacYP707A4 promoter,while transient RNA interference of FacRY1 displayed opposite *** findings reveal a mechanism by which DNA methylation influences ABA catabolism,and participates in light-mediated strawberry ripening.

关键词： ABA catabolism DNA methylation light ripening strawberry

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Unraveling a genetic roadmap for improved taste in the domesticated apple

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Molecular Plant 2021年第9期14卷 1454-1471页

作者： Liao Liao Weihan Zhang Bo Zhang Ting Fang Xiao-Fei Wang Yarning cai collins Ogutu Lei Gao Gang chen Xiaoqing Nie Jinsheng Xu Quanyan Zhang Yiran Ren Jianqiang Yu chukun Wang cecilia H.Deng Baiquan Ma Beibei Zheng chun-Xiang You Da-Gang Hu Richard Espley Kui Lin-Wang Jia-Long Yao andrew c.allan Awais Khan Schuyler S.Korban Zhangjun Fei Ray Ming Yu-Jin Hao Li Li Yuepeng Han cAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Hubei Hongshan LaboratoryWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhan 430074China Agricultural Bioinformatics Key Laboratory of Hubei Province College of InformaticsHuazhong Agricultural UniversityWuhan 430070China center of Economic Botany Core Botanical GardensChinese Academy of SciencesWuhan 430074China University of chinese Academy of Sciences 19A YuquanluBeijing 100049China college of Horticulture Science and Engineering Shandong Agricultural UniversityTai-An 271018China Sino-African Joint Research center Chinese Academy of SciencesWuhan 430074China The New Zealand Institute for Plant&Food Research Limited AucklandNew Zealand School of Biological Sciences University of AucklandPrivate Bag 92019Auckland 1142New Zealand Plant Pathology and Plant-Microbe Biology Section Cornell UniversityGenevaNY 14456USA Department of Natural Resources and Environmental Sciences University of Illinois at Urbana-ChampaignUrbanaIL 61801USA Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL 61801USA

Although taste is an important aspect of fruit quality, an understanding of its genetic control remains elusive in apple and other fruit crops. In this study, we conducted genomic sequence analysis of 497 Malus accessions and revealed erosion of genetic diversity caused by apple breeding and possible independent domestication events of dessert and cider apples. Signatures of selection for fruit acidity and size, but not for fruit sugar content, were detected during the processes of both domestication and improvement. Furthermore, we found that single mutations in major genes affecting fruit taste, including Ma1, MdTDT, and MdSOT2, dramatically decrease malate, citrate, and sorbitol accumulation, respectively, and correspond to important domestication events. Interestingly, Ma1 was identified to have pleiotropic effects on both organic acid content and sugar:acid ratio, suggesting that it plays a vital role in determining fruit taste. Fruit taste is unlikely to have been negatively affected by linkage drag associated with selection for larger fruit that resulted from the pyramiding of multiple genes with minor effects on fruit size. collectively, our study provides new insights into the genetic basis of fruit quality and its evolutionary roadmap during apple domestication, pinpointing several candidate genes for genetic manipulation of fruit taste in apple.

关键词： apple fruit taste organic acids soluble sugars fruit size domestication

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Inflammasome links traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease

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Neural Regeneration Research 2025年第6期20卷 1644-1664页

作者： Gabriela Seplovich Yazan Bouchi Juan Pablo de Rivero Vaccari Jennifer c.Munoz Pareja andrew Reisner Laura Blackwell Yehia Mechref Kevin K.Wang J.Adrian Tyndall Binu Tharakan Firas Kobeissy Department of Surgery Morehouse School of MedicineAtlantaGAUSA Department of Neurobiology Center for NeurotraumaMultiomics&Biomarkers(CNMB)Neuroscience InstituteMorehouse School of MedicineAtlantaGAUSA Department of Neurological Surgery and the Miami Project to cure Paralysis University of Miami Miller School of MedicineMiamiFLUSA Division of Pediatric critical care Department of PediatricsUniversity of Miami Miller School of MedicineMiamiFLUSA Department of Pediatrics Emory UniversityAtlantaGAUSA Department of Neurosurgery Children’s Healthcare of AtlantaAtlantaGAUSA Department of chemistry and Biochemistry Texas Tech UniversityLubbockTXUSA Morehouse School of Medicine AtlantaGAUSA

Traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease are three distinct neurological disorders that share common pathophysiological mechanisms involving neuroinflammation. One sequela of neuroinflammation includes the pathologic hyperphosphorylation of tau protein, an endogenous microtubule-associated protein that protects the integrity of neuronal cytoskeletons. Tau hyperphosphorylation results in protein misfolding and subsequent accumulation of tau tangles forming neurotoxic aggregates. These misfolded proteins are characteristic of traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease and can lead to downstream neuroinflammatory processes, including assembly and activation of the inflammasome complex. Inflammasomes refer to a family of multimeric protein units that, upon activation, release a cascade of signaling molecules resulting in caspase-induced cell death and inflammation mediated by the release of interleukin-1β cytokine. One specific inflammasome, the NOD-like receptor protein 3, has been proposed to be a key regulator of tau phosphorylation where it has been shown that prolonged NOD-like receptor protein 3 activation acts as a causal factor in pathological tau accumulation and spreading. This review begins by describing the epidemiology and pathophysiology of traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease. Next, we highlight neuroinflammation as an overriding theme and discuss the role of the NOD-like receptor protein 3 inflammasome in the formation of tau deposits and how such tauopathic entities spread throughout the brain. We then propose a novel framework linking traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease as inflammasomedependent pathologies that exist along a temporal continuum. Finally, we discuss potential therapeutic targets that may intercept this pathway and ultimately minimize long-term neurological decline.

关键词： Alzheimer's disease caspase-1 chronic traumatic encephalopathy inflammasomes neurodegeneration neuroinflammation NLRP1 NLRP3 pyroptosis tauopathy traumatic brain injury

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Acquired segmental colonic hypoganglionosis in an adult caucasian male:A case report

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World Journal of Gastrointestinal Surgery 2019年第2期11卷 101-111页

作者： allan MF Kwok andrew B Still Kimberly Hart Department of Surgery Wollongong Hospital Department of Anatomical Pathology Wollongong Hospital

BAcKGROUND Hypoganglionosis is a rare condition that most often presents with abnormal gastrointestinal transit and usually arises in early childhood or adolescence. Two types have been described(Type I and Type II). The adult-onset form(acquired hypoganglionosis) is extremely uncommon and is thought to arise due to cellular remodelling as a result of chronic inflammation. It differs from Hirschprung's disease in that there is a reduction in ganglion cells in the colonic neural plexuses as opposed to being completely *** SUMMARY A 31 year-old male presented to hospital with recurrent abdominal pain and vomiting over thirteen months. Abdominal computed tomography scans demonstrated thickening and stranding affecting the transverse, descending and sigmoid colon. Endoscopic appearances were non-specific but confirmed a mixed picture of mucosal inflammation and necrosis in various stages of *** investigations were performed to elucidate an underlying aetiology but neither an infective nor ischaemic cause could be proven. Biopsy features were not typical of inflammatory bowel disease. Due to persistence of his symptoms and failure of medical management, a segmental colectomy was performed. Histological examination of the specimen revealed an unexpected finding of segmental hypoganglionosis. complete surgical excision of the diseased segment of colon was curative and since his operation the patient has had no recurrence of symptoms requiring *** Our case serves to raise awareness of acquired hypoganglionosis as a rare condition that can result from chronic colitis.

关键词： Acquired hypoganglionosis Hirschprung’s disease Adult Ganglion cells Acetylcholinesterase calretinin case report

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An in situ monitoring campaign of a hard rock pillar at great depth within a canadian mine

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Journal of Rock Mechanics and Geotechnical Engineering 2020年第3期12卷 427-448页

作者： Bradley Forbes Nicholas Vlachopoulos Mark S.Diederichs andrew J.Hyett allan Punkkinen Department of Geological Sciences and Geological Engineering Queen’s UniversityKingstonOntarioK7L 3N6Canada Department of civil Engineering Royal Military College of CanadaKingstonOntarioK7K 7B4Canada YieldPoint Inc. KingstonOntarioK7M 4W9Canada Normet canada Ltd. LivelyOntarioP3Y 0B3Canada

A recent research campaign at a canadian nickel-copper mine involved instrumenting a hard rock sill drift pillar with an array of multi-point rod extensometers,distributed optical fibre strain sensors,and borehole pressure cells(BHPcs).The instrumentation spanned across a 15.24 m lengthwise segment of the relatively massive granitic pillar situated at a depth of 2.44 km within the *** May 2016 and March 2017,the pillar’s displacement and pressure response were measured and correlated with mining activities on the same level as the pillar,including:(1)mine-by of the pillar,(2)footwall drift development,and(3)ore body stoping *** displacements of the pillar,the extensometers provided high temporal resolution(logged hourly)and the optical fibre strain sensors provide high spatial resolution(measured every 0.65 mm along the length of each sensor).The combination of sensing techniques allowed centimetre-scale rock mass bulking near the pillar sidewalls to be distinguished from microstrain-scale fracturing towards the core of the ***,the influence and extent of a mine-scale schistose shear zone transecting the pillar was *** converting measured rock mass displacement to velocity,a process was demonstrated which allowed mining activities inducing displacements to be categorised by time-duration and cumulative *** over half of the analysed mining activities,displacements were determined to prolong for over an hour,predominately resulting in submillimetre cumulative displacements,but in some cases multi-centimetre cumulative displacements were *** time-dependent behaviour was more pronounced within the vicinity of the plumb shear *** measurements were also used to assess selected support member load and elongation mobilisation per mining *** was found that a combined static load and elongation capacity of reinforcing members was essential to maintaining excavation stability,while

关键词： Hard rock pillar Rockburst Rock mass bulking Distributed optical fibre strain sensing Extensometer In situ monitoring High stress Dynamic support

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Inaccuracies in the history of a well-known introduction:a case study of the Australian House Sparrow(Passer domesticus)

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chinese Birds 2016年第2期7卷 95-109页

作者： Samuel c.andrew Simon c.Griffith Department of Biological Sciences Macquarie University

Background:Modern ecosystems contain many invasive species as a result of the activity of acclimatisation societies that operated in the second half of the nineteenth century,and these species provide good opportunities for studying invasion ***,to gain insight into the ecological and genetic mechanisms that determine the rate of colonization and adaptation to new environments,we need a good understanding of the history of the introduced species,and a knowledge of the source population,timing,and number of individuals introduced is particularly ***,any inaccuracies in the history of an introduction will affect subsequent assumptions and ***:Focusing on a single well-known species,the House Sparrow(Passer domesticus),we have documented the introduction into Australia using primary sources(*** records and newspaper articles).Results:Our revised history differs in a number of significant ways from previous *** evidence indicates that the House Sparrow was not solely introduced from source populations in England but also from Germany and most strikingly also from India—with the latter birds belonging to a different *** also clarify the distinction between the number released and the number of founders,due to pre-release captive breeding programs,as well as identifying inaccuracies in a couple of well-cited sources with respect to the range expansion of the introduced ***:Our work suggests that caution is required for those studying introductions using the key sources of historical information and ideally should review original sources of information to verify the accuracy of published accounts.

关键词： Acclimatisation Bottlenecks Propagule size Range expansion Hybridisation

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